Contacts of the helix formed by residues 420 - 428 (chain B) in PDB entry 3S95
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 420 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B STU 3.6 31.1 - - + +
418B GLY 4.0 1.1 + - - +
419B GLY* 1.3 74.5 - - - -
421B LEU* 1.3 65.4 + - - +
422B ARG* 3.6 4.2 + - - +
423B GLY* 3.0 28.8 + - - -
424B ILE* 3.3 13.9 + - - +
463B SER 3.8 11.7 - - - -
464B HIS* 3.4 28.0 + - + +
466B CYS 3.4 6.1 - - - -
467B LEU* 3.9 5.8 - - + -
468B VAL* 4.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B GLY 3.8 0.6 + - - -
420B THR* 1.3 73.2 - - - +
422B ARG* 1.3 66.2 + - - +
424B ILE* 3.0 6.6 + - + +
425B ILE* 2.8 37.4 + - + +
440B PHE* 3.7 37.7 - - + -
444B ILE* 3.8 29.4 - - + -
463B SER* 3.4 13.2 + - - +
466B CYS* 2.8 23.1 + - + +
468B VAL* 3.8 17.4 - - + +
474B VAL* 5.3 0.7 - - + -
538B VAL* 3.8 20.4 - - + -
542B ILE* 4.2 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B THR* 3.1 6.2 - - - +
421B LEU* 1.3 78.0 - - - +
423B GLY* 1.3 62.9 + - - +
425B ILE* 3.2 17.1 + - - +
426B LYS* 3.0 45.4 + - + +
463B SER* 2.9 30.5 + - - +
464B HIS* 3.6 25.4 - - + +
515B TRP* 6.1 0.2 - - - -
541B GLU* 4.0 15.5 - - - -
545B ARG 5.2 1.4 + - - -
546B VAL* 4.1 6.9 + - - +
547B ASN* 3.7 40.8 + - - +
641B TRS 3.0 49.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B THR* 3.0 20.8 + - - -
422B ARG* 1.3 77.0 - - - +
424B ILE* 1.3 62.6 + - - +
426B LYS* 3.5 14.6 + - - +
427B SER* 3.4 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B GLY* 4.1 17.7 - - - +
420B THR 3.3 12.7 + - - +
421B LEU* 3.0 11.9 + - + +
423B GLY* 1.3 73.9 - - - +
425B ILE* 1.3 67.6 + - - +
427B SER* 2.6 29.2 + - - +
428B MET* 3.2 20.4 + - + +
432B TYR* 3.9 25.6 - - + +
440B PHE* 4.2 7.4 - - + -
468B VAL* 4.3 23.3 - - + -
472B LYS* 6.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B LEU* 2.8 35.1 + - + +
422B ARG* 3.7 18.6 - - - +
424B ILE* 1.3 77.6 - - - +
426B LYS* 1.3 61.7 + - - +
428B MET* 3.1 42.2 + - + +
463B SER* 4.6 2.2 - - - -
538B VAL 4.9 0.2 - - - +
541B GLU* 3.6 47.3 - - + +
542B ILE* 3.9 21.5 - - + +
545B ARG* 3.8 24.3 - - + +
546B VAL 4.3 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ARG* 3.0 41.4 + - - +
423B GLY* 3.6 15.5 - - - +
424B ILE 3.2 0.2 - - - -
425B ILE* 1.3 76.8 - - - +
427B SER* 1.3 59.1 + - - +
428B MET 3.6 2.6 + - - +
641B TRS 3.0 48.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLY 3.4 10.0 + - - -
424B ILE* 2.6 29.9 + - - +
426B LYS* 1.3 78.4 - - - +
428B MET* 1.3 64.7 + - - +
429B ASP* 3.4 3.1 + - - +
432B TYR* 5.3 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ILE* 3.2 18.8 + - + +
425B ILE* 3.1 36.6 + - + +
426B LYS 3.3 2.6 - - - +
427B SER* 1.3 78.8 - - - +
429B ASP* 1.3 62.4 + - - +
432B TYR* 3.6 51.4 - - + -
437B ARG* 4.2 17.3 - - + -
440B PHE* 3.9 19.1 - - + -
542B ILE* 4.6 5.4 - - + +
545B ARG* 2.8 45.0 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il